Even before the microbiome craze — the hope that the bacteria in your gut holds the key to good health — people were ingesting cultures of living micro-organisms to treat a host of conditions. These probiotics have become so popular that they’re being marketed in foods, capsules and even beauty products.

Probiotics have the potential to improve health, including by displacing potentially harmful bugs. The trouble is that the proven benefits involve a very small number of conditions, and probiotics are regulated less tightly than drugs. They don’t need to be proved effective to be marketed, and the quality control can be lax.

In a recent article in JAMA Internal Medicine, Pieter Cohen, an associate professor of medicine at Harvard Medical School, urges us to consider the harms as well as the benefits. Among immune-compromised individuals, for instance, probiotics can lead to infections.

Consumers can’t always count on what they’re getting. From 2016 to 2017, the Food and Drug Administration inspected more than 650 facilities that produce dietary supplements, and determined that more than 50 percent of them had violations. These included issues with the purity, strength and even the identity of the promised product.

Given all of this, what are the benefits? The most obvious use of probiotics would be in the treatment of gastrointestinal disorders, given that they are focused on gut health. There have been many studies in this domain, so many that early this year the journal Nutrition published a systematic review of systematic reviews on the subject.

The takeaway: Certain strains were found useful in preventing diarrhea among children being prescribed antibiotics. A 2013 review showed that after antibiotic use, probiotics help prevent Clostridium difficile-associated diarrhea. A review focused on acute infectious diarrhea found a benefit, again for certain strains of bacteria at controlled doses. There’s also evidence that they may help prevent necrotizing enterocolitis (a serious gastrointestinal condition) and death in preterm infants.

Those somewhat promising results — for very specific uses of very specific strains of bacteria in very specific instances — are just about all the “positive” results you can find.

“Sometimes small studies suggest strains work, but when a larger more well-done study is performed, they no longer seem to,” Dr. Cohen said.

When research is done on probiotics, it usually involves a specific organism, defined by genus, species and even strain. When used in studies, they are pure and carefully dosed. But when we buy probiotics off the shelf, especially when they are in food products, we often have no idea what we’re getting.

Yet that’s how probiotics are often offered. They can be distributed in the United States as food, supplements or drugs. The regulations for each are very different. Most people looking for probiotics don’t see the distinctions. Ideally, the ways in which we use and consume probiotics would conform to the data and evidence that back them up. That rarely happens.

Further, there’s still a lot we don’t know. A recent study published in Cell compared how the microbiome of the gut reconstituted itself after antibiotic treatment with and without probiotic administration. The researchers found that probiotics (which might have improved diarrhea symptoms) led to a significant delay in microbiome reconstitution, if it occurred at all. And — again — this study was with purified strains of bacteria, which is not what you’re getting in probiotic-containing food.

Of course, people with no immune deficiencies should feel free to eat yogurt and sauerkraut, which can absolutely be part of a healthy diet. Eat them because they’re delicious, and most likely better for you than many other foods, not because of any health claims.

“It’s important that consumers understand that all those nicely labeled containers on store shelves are not vetted by the F.D.A.,” Dr. Cohen said. “They’re not carefully watching over the probiotic space, leaving consumers to be the guinea pigs for these science experiments.”

For too long we’ve assumed that probiotics are doing some good and little harm. That might be true for some, but it’s not assured in the current environment.